Powerful Model

Nothing stays still. Even at the atomic level – especially at the atomic level – forces between particles keep them wriggling, even when locked in a relatively 'stable' structure. In these computer simulations, researchers mimic tiny proteins in the conical outer shell or capsid of the human immunodeficiency virus. Each pentamer (green) or hexamer (cream) structure is built from smaller building blocks called monomers – the model traces their jostling movements over nanoseconds. Simulating so many moving parts at once is a huge challenge for computer power, so the research team uses new methods to balance the ‘granularity’ of the model – how abstracted the molecular details are from real life – with how faithfully they mimic the overall biological behaviour. New algorithms using a 'coarser' granularity require less computer power (and energy), opening up the power similar simulations to more research groups worldwide.

Written by John Ankers

• Video from work by Alexander J. Bryer, Juan S. Rey & Juan R. Perilla
• Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
• Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)
• Published in Nature Communications, April 2023